7EC3

Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)

• PDB DOI: https://doi.org/10.2210/pdb7EC3/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus USA300, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-03-11 Released: 2022-03-16 
• Deposition Author(s): Kim, D.-G., Baek, I., Lee, Y., Kim, H.S.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.240 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 122.83 kDa 
• Atom Count: 8,579 
• Modelled Residue Count: 1,014 
• Deposited Residue Count: 1,026 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl transferase, group 1 family protein	A, B [auth C]	505	Staphylococcus aureus subsp. aureus USA300	Mutation(s): 0  Gene Names: SAUSA300_0550
UniProt
Find proteins for Q2G0L2 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0L2  Go to UniProtKB:  Q2G0L2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE	C [auth D], D [auth G]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	E [auth A], G [auth C]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAG (Subject of Investigation/LOI)	F [auth A], H [auth C], I [auth D], J [auth D], K [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.240 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.201	α = 90
b = 130.568	β = 90
c = 189.854	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Kim, D.-G., Baek, I., Lee, Y., Kim, H.S.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020R1C1C1009512
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017R1C1B2012225
National Research Foundation (NRF, Korea)	Korea, Republic Of	2015R1D1A4A01020265

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2022-10-12
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description